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Hello dear Freesurfer developers, nice to e-meet you and thank you for working on this open source software!
I am trying to produce a 3D file of a brain. The command I am trying to run is recon-all and here is the error I get:
*CORRECTING DEFECT 57 (vertices=33394, convex hull=9966) Excessive topologic defect encountered: could not allocate 140742253 edges for retessellation Cannot allocate memory*
The version I am using is: freesurfer-Linux-centos4-stable-pub-v5.3.0 The platform is Red Hat 64-bit running in a Virtual box with 7835mb allocated memory. You will find the corresponding log file attached.
Isn't it surprising that I don't have enough memory with 7835mb allocated? Sorry, I am new to Freesurfer and there might be something I didn't get. Thank you very much in advance for your help, Regards,
Gabriel Tapia https://gabrieltapia.fr/ www.Partage3D.fr http://partage3d.fr/ +33 6 62 90 11 67
Hi Gabriel,
that is a huge defect and generally means something major has gone wrong. Look at the lh or rh.orig.nofix and the corresponding ?h.inflated.nofix over the wm.mgz file to see what is wrong (usually something like a big chunk of skull is left over and connected to the surface, sometimes through orbital fat in the eye sockets)
If you can't sort it out let us know and we will help cheers Bruce
On Tue, 25 Feb 2020, Gabriel Tapia wrote:
External Email - Use Caution
Hello dear Freesurfer developers, nice to e-meet you and thank you for working on this open source software!
I am trying to produce a 3D file of a brain. The command I am trying to run is recon-all and here is the error I get: CORRECTING DEFECT 57 (vertices=33394, convex hull=9966) Excessive topologic defect encountered: could not allocate 140742253 edges for retessellation Cannot allocate memory
The version I am using is: freesurfer-Linux-centos4-stable-pub-v5.3.0 The platform is Red Hat 64-bit running in a Virtual box with 7835mb allocated memory. You will find the corresponding log file attached.
Isn't it surprising that I don't have enough memory with 7835mb allocated? Sorry, I am new to Freesurfer and there might be something I didn't get. Thank you very much in advance for your help, Regards,
Gabriel Tapia www.Partage3D.fr +33 6 62 90 11 67
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Hello Bruce thank you for your quick reply, Where should I look to get all these files? The idea to check them is to confirm that the MRI went wrong at some point, right? Thanks,
Gabriel Tapia https://gabrieltapia.fr/ www.Partage3D.fr http://partage3d.fr/ +33 6 62 90 11 67
Le mar. 25 févr. 2020 à 04:09, Bruce Fischl fischl@nmr.mgh.harvard.edu a écrit :
Hi Gabriel,
that is a huge defect and generally means something major has gone wrong. Look at the lh or rh.orig.nofix and the corresponding ?h.inflated.nofix over the wm.mgz file to see what is wrong (usually something like a big chunk of skull is left over and connected to the surface, sometimes through orbital fat in the eye sockets)
If you can't sort it out let us know and we will help cheers Bruce
On Tue, 25 Feb 2020, Gabriel Tapia wrote:
External Email - Use CautionHello dear Freesurfer developers, nice to e-meet you and thank you for working on this open source software!
I am trying to produce a 3D file of a brain. The command I am trying to run is recon-all and here is the error I get: CORRECTING DEFECT 57 (vertices=33394, convex hull=9966) Excessive topologic defect encountered: could not allocate 140742253 edges for retessellation Cannot allocate memory
The version I am using is: freesurfer-Linux-centos4-stable-pub-v5.3.0 The platform is Red Hat 64-bit running in a Virtual box with 7835mb allocated memory. You will find the corresponding log file attached.
Isn't it surprising that I don't have enough memory with 7835mb
allocated?
Sorry, I am new to Freesurfer and there might be something I didn't get. Thank you very much in advance for your help, Regards,
Gabriel Tapia www.Partage3D.fr +33 6 62 90 11 67
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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They are all in the output folder of the subject.
The noxfix files are surfaces (in <subject>/surf/), the mgz file is a volume (in <subject>/mri/).
Tim
On February 25, 2020 at 4:24 AM Gabriel Tapia gabriel@partage3d.fr wrote:
External Email - Use CautionHello Bruce thank you for your quick reply, Where should I look to get all these files? The idea to check them is to confirm that the MRI went wrong at some point, right? Thanks,
Gabriel Tapia https://gabrieltapia.fr/ www.Partage3D.fr http://partage3d.fr/ +33 6 62 90 11 67
Le mar. 25 févr. 2020 à 04:09, Bruce Fischl fischl@nmr.mgh.harvard.edu a écrit :
Hi Gabriel,
that is a huge defect and generally means something major has gone wrong. Look at the lh or rh.orig.nofix and the corresponding ?h.inflated.nofix over the wm.mgz file to see what is wrong (usually something like a big chunk of skull is left over and connected to the surface, sometimes through orbital fat in the eye sockets)
If you can't sort it out let us know and we will help cheers Bruce
On Tue, 25 Feb 2020, Gabriel Tapia wrote:
External Email - Use CautionHello dear Freesurfer developers, nice to e-meet you and thank you for working on this open source software!
I am trying to produce a 3D file of a brain. The command I am trying to run is recon-all and here is the error I get: CORRECTING DEFECT 57 (vertices=33394, convex hull=9966) Excessive topologic defect encountered: could not allocate 140742253 edges for retessellation Cannot allocate memory
The version I am using is: freesurfer-Linux-centos4-stable-pub-v5.3.0 The platform is Red Hat 64-bit running in a Virtual box with 7835mb allocated memory. You will find the corresponding log file attached.
Isn't it surprising that I don't have enough memory with 7835mb
allocated?
Sorry, I am new to Freesurfer and there might be something I didn't get. Thank you very much in advance for your help, Regards,
Gabriel Tapia www.Partage3D.fr +33 6 62 90 11 67
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Gabriel
they are in the subject's directory. Have you gone through the FS tutorials on our wiki? That would be a good place to start
cheers Bruce On Tue, 25 Feb 2020, Gabriel Tapia wrote:
External Email - Use Caution
Hello Bruce thank you for your quick reply, Where should I look to get all these files? The idea to check them is to confirm that the MRI went wrong at some point, right? Thanks,
Gabriel Tapia www.Partage3D.fr +33 6 62 90 11 67
Le mar. 25 févr. 2020 à 04:09, Bruce Fischl fischl@nmr.mgh.harvard.edu a écrit : Hi Gabriel,
that is a huge defect and generally means something major has gone wrong. Look at the lh or rh.orig.nofix and the corresponding ?h.inflated.nofix over the wm.mgz file to see what is wrong (usually something like a big chunk of skull is left over and connected to the surface, sometimes through orbital fat in the eye sockets) If you can't sort it out let us know and we will help cheers Bruce On Tue, 25 Feb 2020, Gabriel Tapia wrote: > > External Email - Use Caution > > Hello dear Freesurfer developers, nice to e-meet you and thank you for > working on this open source software! > > I am trying to produce a 3D file of a brain. > The command I am trying to run is recon-all and here is the error I get: > CORRECTING DEFECT 57 (vertices=33394, convex hull=9966) > Excessive topologic defect encountered: could not allocate 140742253 > edges for retessellation > Cannot allocate memory > > The version I am using is: freesurfer-Linux-centos4-stable-pub-v5.3.0 > The platform is Red Hat 64-bit running in a Virtual box with 7835mb > allocated memory. > You will find the corresponding log file attached. > > Isn't it surprising that I don't have enough memory with 7835mb allocated? > Sorry, I am new to Freesurfer and there might be something I didn't get. > Thank you very much in advance for your help, > Regards, > > Gabriel Tapia > www.Partage3D.fr > +33 6 62 90 11 67 > >_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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